GABPB1

protein-coding

GA binding protein transcription factor subunit beta 1, the group of Ankyrin repeat domain containing

Gene summary

This gene encodes the GA-binding protein transcription factor, beta subunit. This protein forms a tetrameric complex with the alpha subunit, and stimulates transcription of target genes. The encoded protein may be involved in activation of cytochrome oxidase expression and nuclear control of mitochondrial function. The crystal structure of a similar protein in mouse has been resolved as a ternary protein complex. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

GABPB2

MANE transcript

NM_016654.5

Inheritance

—

ClinVar variants

U:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr15:50,275,389-50,355,408

External References & Databases

Ensembl (ENSG00000104064)

Transcript & Mutation Effects

hg38 • Region Span ~80.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GABPB1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 11

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016654.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	19	0	0	19

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 91 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016654.5	RefSeq	NP_057738.1	8	MANE Select
ENST00000380877.8	Ensembl	ENSP00000370259.3	8	MANE Select
NM_001320910.2	RefSeq	NP_001307839.1	8	Standard
NM_001320915.2	RefSeq	NP_001307844.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Myometrial Relaxation and Contraction Pathways
Hematopoietic Stem Cell Gene Regulation by GABP alpha-beta Complex
Mitochondrial Gene Expression
Transcriptional activation of mitochondrial biogenesis
Mitochondrial biogenesis

Biological Process

regulation of transcription by RNA polymerase II
mitochondrion organization
positive regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity
protein binding
transcription regulatory region DNA binding
protein heterodimerization activity

Cellular Component

nucleus
nucleoplasm
cytoplasmic ribonucleoprotein granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000220429
Coding exons: 8
Length: 78217
Individuals with no LoFs: 124199
Homozygous LoFs: 4
Heterozygous LoFs: 969
Defined: 125172
p: 0.00389

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.93	90	209	0.430	0.0000101	2545
Missense (PolyPhen)		17	70.52	0.24107		898
Synonymous	1.38	57	71.9	0.793	0.00000342	809
Loss of Function	3.64	3	21.0	0.143	0.00000130	222

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0018	0.0018	notable
Latino/Admixed American	0.0030	0.0030	notable
Ashkenazi Jewish	0.012	0.012	notable
East Asian	0	0.0	absent
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.0042	0.0042	notable
South Asian	0.0071	0.0071	notable
Other	0.0047	0.0048	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor capable of interacting with purine rich repeats (GA repeats). Necessary for the expression of the Adenovirus E4 gene. {ECO:0000269|PubMed:10675337, ECO:0000269|PubMed:8816484}.;

Recessive Scores

pRec: 0.194

Intolerance Scores

LoFtool: 0.507
RVIS EVS: 0.35
RVIS percentile EVS: 73.97

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium